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Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing.

ABSTRACT: The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived from a breast cancer cell line-which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations-and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with >2,000-fold coverage, spanning 82% of genomic regions with high confidence. Although the gDNA reference samples are not representative of primary cancer cells from a clinical sample, when setting up a sequencing pipeline, they not only minimize potential biases from technologies, assays and informatics but also provide a unique resource for benchmarking 'tumor-only' or 'matched tumor-normal' analyses.

SUBMITTER: Fang LT

PROVIDER: S-EPMC8532138 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature

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Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing.

Fang Li Tai LT Zhu Bin B Zhao Yongmei Y Chen Wanqiu W Yang Zhaowei Z Kerrigan Liz L Langenbach Kurt K de Mars Maryellen M Lu Charles C Idler Kenneth K Jacob Howard H Zheng Yuanting Y Ren Luyao L Yu Ying Y Jaeger Erich E Schroth Gary P GP Abaan Ogan D OD Talsania Keyur K Lack Justin J Shen Tsai-Wei TW Chen Zhong Z Stanbouly Seta S Tran Bao B Shetty Jyoti J Kriga Yuliya Y Meerzaman Daoud D Nguyen Cu C Petitjean Virginie V Sultan Marc M Cam Margaret M Mehta Monika M Hung Tiffany T Peters Eric E Kalamegham Rasika R Sahraeian Sayed Mohammad Ebrahim SME Mohiyuddin Marghoob M Guo Yunfei Y Yao Lijing L Song Lei L Lam Hugo Y K HYK Drabek Jiri J Vojta Petr P Maestro Roberta R Gasparotto Daniela D Kõks Sulev S Reimann Ene E Scherer Andreas A Nordlund Jessica J Liljedahl Ulrika U Jensen Roderick V RV Pirooznia Mehdi M Li Zhipan Z Xiao Chunlin C Sherry Stephen T ST Kusko Rebecca R Moos Malcolm M Donaldson Eric E Tezak Zivana Z Ning Baitang B Tong Weida W Li Jing J Duerken-Hughes Penelope P Catalanotti Claudia C Maheshwari Shamoni S Shuga Joe J Liang Winnie S WS Keats Jonathan J Adkins Jonathan J Tassone Erica E Zismann Victoria V McDaniel Timothy T Trent Jeffrey J Foox Jonathan J Butler Daniel D Mason Christopher E CE Hong Huixiao H Shi Leming L Wang Charles C Xiao Wenming W

Nature biotechnology 20210909 9

The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived from a breast cancer cell line-which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations-and a matched lymphoblastoid cell line. We partially valid ...[more]

PMID: 34504347

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Project description:BackgroundCommunity engagement or community involvement in Aboriginal health research is a process that involves partnering, collaborating and involving Aboriginal and Torres Strait Islander people or potential research participants to empower them to have a say in how research with Aboriginal communities is conducted. In the context of Aboriginal health, this is particularly important so that researchers can respond to the priorities of the community under study and conduct research in a way that is respectful of Aboriginal cultural values and beliefs. One approach to incorporating the principals of community engagement and to ensure cultural oversight and guidance to projects is to engage a community reference group. The aim of this study was to describe the process of establishing an Aboriginal community reference group and terms of reference. The community reference group was established to guide the research activities of a newly formed research collaboration aiming to to develop osteoarthritis care that meets the needs of Aboriginal and Torres Strait Islander people in Australia.MethodsAdopting a Participatory Action Research approach, this two-phase study was conducted in Victoria, Australia. In phase one, semi-structured research yarns (a cultural form of conversation used as a data gathering tool) were conducted collaboratively by Aboriginal and non-Aboriginal co-investigators to explore Aboriginal health stakeholder perspectives on establishing a community reference group and terms of reference. In phase two, recommendations in phase one were identified to invite members to participate in the community reference group and to ratify the terms of reference through a focus group. Data were analyzed using a framework analysis approach.ResultsThirteen people (eight female, four male) participated in phase one. Participants represented diverse professional backgrounds including physiotherapy, nursing, general practice, health services management, hospital liaison, cultural safety education, health research and the arts. Three themes were identified in phase one; Recruitment and Representation (trust and relationships, in-house call-outs, broad-spectrum expertise and Aboriginal majority); Purpose (community engagement, research steering, knowledge dissemination and advocacy) and; Function and Logistics (frequency and format of meetings, size of group, roles and responsibilities, authority, communication and dissemination). In phase two, six Aboriginal people were invited to become members of the community reference group who recommended changes which were incorporated into the seven domains of the terms of reference.ConclusionThe findings of this study are captured in a 10-step framework which describes practical strategies for establishing a community reference group and terms of reference in Aboriginal health research.

Dataset Information

Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing.

Publications

Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing.

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